Shepard's True Choice
by Dark-Ninja92
Summary: What if Shepard chose differently at the crucible, seeing a truth that would change everything? this is a mixture of refusal and indoctrination theory. will contain Shep x tali


Hey everyone, Dark-ninja92 here. This is my second story so there still may be some problem areas, but hopefully the good outweighs the bad. This will be a mix of indoctrination theory and refusal ending and will build off that. And before you start wondering, this isn't made out of hatred for the endings of mass effect, I'm not really a fan of them, but I don't hate them. Anyway, I don't own mass effect, otherwise there would have been a Shepard epilogue after the credits instead of just that breath scene. Also, I don't own any of the characters, not yet anyway, I may add some. And of course spoilers will be present, but at this point, I doubt that would be a problem. Add in any other warnings and such that I forgot. Oh, and here's my Shepard that I'm using, just FYI.

Gender : Male

Class : infiltrator

Background : Spacer

Service history : war hero

Alignment : paragon with minor renegade

Love interest : Tali

If there's anything I forgot, you'll figure it out anyway, oh, and ps, my Shepard is a bit more of a smartass than what's in the game. Story, start!

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Prologue

Shepard stood at the three-way that led to his choices on how to defeat the reapers. Each choice had a cost but a decision had to be made. Control, Destroy, or Synthesis. Just as Shepard was about to start walking, images flashed through his head, the future consequences of his decision.

Control would bring peace at the cost of Shepard himself, becoming leader of the reapers and rocketing galactic civilization forward. With the reapers, much of the damage could be repaired, and the technology behind things like the relays would be understood. But it would not last, as the one leading the reapers would not really be him but an AI created from his mind. Eventually the reapers "logic" would take over and break down emotions and morality and the reaper's cycle would start again.

Destroy had the highest price, Costing not only Shepard's life, but that of EDI and synthetic life as well. The relays would become too damaged to function and technology would be set back greatly. But it would end the reapers, ensuring that they would never endanger anyone again. But this too, would not last. While many synthetics would be destroyed, the strongest would survive, seeing everything as a betrayal from organics. They would escape and hide, building up forces until one day they could attack and become the next reapers, with the goal of exterminating organic life, so that synthetics could flourish.

Synthesis would only take Shepard's life, and would turn all life into a hybrid of synthetic and organic. Peace would come as the reapers would no longer have purpose and would leave. Many forms of life would benefit, such as the Quarians no longer needing their suits due to synthetic enhancements. But this was also a flawed solution. As everyone's DNA was rewritten using what was created from Shepard, a part of his DNA would be in all life, genetic diversity would be greatly reduced, affecting following generations. The path to immortality would be reached eventually, making reproduction unnecessary, but not before a permanent scar would be left in the galactic gene pool. And even then, new organic life would eventually come to exist, and everything would begin again.

As the images faded, Shepard stopped, trying to process what he just saw. At this the starchild(or whatever that reaper AI is called) spoke to him.

"What is the problem? You need to make your decision before it's too late."

"I- I can't, none of these actually stop the reapers, they just delay them. And the consequences, I may as well be doing the reapers' job for them."

"That's true, all of these choices only delay the inevitable, in the end the cycle cannot be stopped"

"But then what has all this been for? Nothing?! There has to be some way to end this permanently. It's like the choices are-"

And then things started to come together in his mind, the recent events, the choices, everything.

" This is all a lie, isn't it, nothing here makes sense!"

"What are you talking about human, you just need to hurry and make your decision"

"No, because none of this is real. It can't be, I was the first to enter the beam to the citadel, and even though there was only one path to the citadel's arm control, Anderson still made it before me without passing me. And this room, why the hell would it be designed like this? The main control panel is all the way over there, one path leads straight into the crucible's beam itself, and another leads directly to the one weak point in the crucible's power regulation. My pistol seems to have an endless clip, and how is it that you manage to have the appearance of the one child that I've been seeing in my nightmares? It's been one thing after another since…since…since I was hit by harbinger's beam! There should have been no way I could have survived that when reaper beams can pierce starships! Not unless he intended to keep me alive for some reason. This is a trick, I refuse to pick your choices, civilization will fight on it's own if it has to."

At that point, starchild had its response, and in an all too familiar low booming voice.

"So be it"

The hologram faded, and a humanoid figure rose onto the spot where starchild stood. The figure was similar to Shepard in shape and build, but was synthetic, and had five reaper arms sticking out of the back, and the face was simply a blank plate, with two glowing yellow eyes. Shepard quickly felt all the pain leave his body, and stood upright, no longer being hindered by false injuries.

"I knew it, this was your attempt at indoctrination? But why go to such effort for one individual?"

"You would be unable to comprehend, but it does not matter, your resistance will end here"

At that, Harbinger shot a blast at Shepard from one of the reaper arms, and although Shepard dodged it, it hit a part of the walkway behind him, and caused the entire section to fall, with Shepard falling with it. He landed and rolled out of the way as pieces of the walkway crashed around him, with Harbinger following soon after, opening fire at Shepard. Shepard took cover behind nearby debris and fired a few shots at Harbinger, but had little to no effect.

"Damn it. This pistol just isn't enough. I need something stronger, but I can pull weapons out of thin air,… or can I. this is all in my mind, maybe if I focus."

In an instant, Shepard felt weight add onto his back, he reached back and pulled out a black widow. He peered out from cover, and took aim. The first few shot's still didn't do much damage, but when one shot his the core in one of the reaper arms, it caused an overload and blew off the arm. Shepard ducked and weaved from cover to cover, repeating the process. As he blew off the last arm, Harbinger let out a loud reaper growl and his chest opened, revealing a large firing chamber like the reaper Shepard fought on Rannoch. One blast blew through the nearby debris, and narrowly missed Shepard. As Harbinger was charging a second shot, Shepard took the opportunity to fire round after round into the firing chamber. Just before Harbinger could fire, Shepard fired one final shot, and broke through the firing chamber, destroying Harbinger. Shepard's vision soon faded to black, and he awoke with a sharp breath, and feeling immense pain from his body. He didn't know how long he was there, but he snapped to his senses when he heard the voice of someone dear to him.

"Keelah Shepard! You're alive! Garrus, quick! Get the medigel!"

"Don't worry Tali, I got it."

Garrus and Tali spread the medigel to the worst areas, and helped Shepard up, who was still barely able to stand.

" Come on Shepard, we need to get you out of here."

"No, the Citadel needs to be opened"

"Shepard, come on, you can barely stand! If we don't get you real medical help soon you might not make it. And besides, the beam to the citadel is gone."

"No Garrus, look. It's opening up again, if we don't go now, there might not be another chance. We've worked long and hard to bring the galaxy together to fight the reapers, and I'm going to make sure it ends."

"Damn it Shepard! Sometimes there's just no stopping you is there? I can tell you're not going to back down on this, so I guess I'll give you a hand so you can walk. Tali, you want to get him on his other side? We'll get you to the Citadel, Shepard."

"Garrus, we may have a problem with that, look!"

Shepard and Garrus turnd to look at what Tali was pointing at, and saw a brute headed for them. Just as it was gaining momentum, a shot slammed against it's head, knocking it back. A moment later, a second shot took it's head off. Garrus looked to the source of the shot, and saw a someone only he would remember, carrying a widow rifle.

"Sidonis!?"

"Garrus, I told you I'd make it up to you one day, and I'm going to do that now, a group of reaper forces are coming, I'll hold them off, you get the Commander to that beam."

Just as Garrus, Tali, and Shepard started moving, a group of husks came over the top of the hill, and Sidonis switched to a phaeston he was carrying, opening fire instantly.

"Hurry up and go! I don't know how long I'll be able to hold them off!"

The trio headed for the beam as fast as they could, and just before they entered the beam, they heard they heard a brute charging, widow shots, and cries of pain from Sidonis. When they exited the beam, they were in the central room, where the citadel arm control was, but this time, there was no Anderson or Illusive man. Shepard limped to the panel and opened the Citadel arms to let in the Crucible. Just like before, the spot where Shepard was rose up to a higher level, but instead of the starchild and the three choices, there was a single control panel. Shepard approached it and set the Crucible to fire. Jus before Shepard finished, Harbinger appeared.

"Human, you cannot fathom the consequences of what you are about to do."

"Save it, this ends today."

Shepard fired the crucible, and a burst of purple energy surged forth, overloading the reapers, the smaller and weaker one actually self-destructing.

" Human, we were your salvation. Without us, you are-re-re"

Harbinger broke down, as the crucible finished it's work. The reaper drifted away, everything silent. Shepard looked around, seeing that all the remaining reapers were the same as harbinger, dead and silent, as the remaining galactic forces moved in and finished them off. As Shepard took in the sight that signaled the end of the reaper invasion, his vision faded to black and passed out, his body finally giving into the pain, injuries, and exhaustion.

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That's it for the first chapter, and the end of it for those of you with low ems points. If you like this, let me know what you think, and any areas that I need to improve.


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